POPC @ 310K, varying amounts of NaCl. Slipids with ECC-scaled ions

<p>Simulations of a POPC bilayer with varying amounts of NaCl.<br> These simulations were performed as a part of the NMRlipids<br> project (http://nmrlipids.blogspot.fi). The goal was to study&nbsp;<br> the effect of salt on the order parameters of the lipid head&nbsp;<br> group and the glycerol backbone. The obtained results are&nbsp;<br> reported in the blog.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is&nbsp;<br> simulated in the presence of NaCl. Concentrations of 130, 300,&nbsp;<br> 500, 750, and 1000 mM are employed. The Slipids model [1&ndash;3] is&nbsp;<br> employed for lipids, tip3p model for water, and the recent ion&nbsp;<br> parameters by Kohagen et al. [4] for NaCl.&nbsp;</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;</p> <p>The files are named based on the concentration of NaCl<br> and are in GROMACS format. Trajectories (.xtc) are&nbsp;<br> 100 ns long with data saved every 100 ps. Additionally,<br> initial structures (.gro), topology (.top), index (.ndx)<br> and binary run input files for GROMACS v. 4.6&ndash;&gt; (.tpr)<br> are provided. The run parameter file (.mdp) is general<br> for all systems.</p> <p>&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;</p> <p>[1] Derivation and Systematic Validation of a Refined&nbsp;<br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. J&auml;mbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>&nbsp;</p> <p>[2] An Extension and Further Validation of an All-Atomistic&nbsp;<br> Force Field for Biological Membranes<br> Joakim P. M. J&auml;mbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>&nbsp;</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. J&auml;mbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p> <p>&nbsp;</p> <p>[4] Accounting for Electronic Polarization Effects in Aqueous Sodium&nbsp;<br> Chloride via Molecular Dynamics Aided by Neutron Scattering<br> Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br> The Journal of Physical Chemistry B Article ASAP<br> DOI: 10.1021/acs.jpcb.5b0522</p>